From 700776f759b59fb628dd046cee3ff389cac5987f Mon Sep 17 00:00:00 2001 From: ameynert Date: Tue, 30 Mar 2021 16:11:15 +0100 Subject: [PATCH] Change to shared Singularity cache --- docs/eddie.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/eddie.md b/docs/eddie.md index cb78d71..e5dbe5c 100644 --- a/docs/eddie.md +++ b/docs/eddie.md @@ -35,13 +35,13 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul ## Singularity set-up -Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. +Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path below. If some containers for your pipeline run are not present, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again. ```bash module load singularity -export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity/nf-core-rnaseq_v3.0" +export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity" ``` Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.